Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1107276178:

Variant ID: vg1107276178 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7276178
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.82, T: 0.18, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

CGGTATTTGTCGAGGAGTGGTCCTCTCTAGCAGGAGGTCGTGAGATCCCCCTTTGTGAGTTCGGCCGGGGGATAAGGCGCAATGATCAAGAGCGTGTCTC[C/T]
GCTTCGGATCTAGCTGGTGAGATTCTTCGCAAGAGAGTGAGAAACAAGGGATTATACAGGTTCGGGCCACTGGGGAGCGTAACACCCTACTCCTGTGTAT

Reverse complement sequence

ATACACAGGAGTAGGGTGTTACGCTCCCCAGTGGCCCGAACCTGTATAATCCCTTGTTTCTCACTCTCTTGCGAAGAATCTCACCAGCTAGATCCGAAGC[G/A]
GAGACACGCTCTTGATCATTGCGCCTTATCCCCCGGCCGAACTCACAAAGGGGGATCTCACGACCTCCTGCTAGAGAGGACCACTCCTCGACAAATACCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.40%	27.80%	0.87%	38.89%	NA
All Indica	2759	35.60%	1.60%	1.49%	61.33%	NA
All Japonica	1512	18.30%	76.00%	0.00%	5.69%	NA
Aus	269	88.10%	1.50%	0.00%	10.41%	NA
Indica I	595	66.90%	0.30%	0.67%	32.10%	NA
Indica II	465	12.70%	0.20%	2.37%	84.73%	NA
Indica III	913	24.90%	1.30%	1.86%	71.96%	NA
Indica Intermediate	786	37.80%	3.80%	1.15%	57.25%	NA
Temperate Japonica	767	28.60%	69.40%	0.00%	2.09%	NA
Tropical Japonica	504	2.20%	87.30%	0.00%	10.52%	NA
Japonica Intermediate	241	19.50%	73.40%	0.00%	7.05%	NA
VI/Aromatic	96	6.20%	91.70%	0.00%	2.08%	NA
Intermediate	90	34.40%	32.20%	0.00%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1107276178	C -> T	LOC_Os11g12830.1	downstream_gene_variant ; 2420.0bp to feature; MODIFIER	silent_mutation	Average:43.9; most accessible tissue: Callus, score: 74.189	N	N	N	N
vg1107276178	C -> T	LOC_Os11g12810-LOC_Os11g12830	intergenic_region ; MODIFIER	silent_mutation	Average:43.9; most accessible tissue: Callus, score: 74.189	N	N	N	N
vg1107276178	C -> DEL	N	N	silent_mutation	Average:43.9; most accessible tissue: Callus, score: 74.189	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107276178	2.75E-06	3.99E-06	mr1890_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251